Egypt's military junta is facing its biggest crisis of legitimacy, as tens of thousands of protesters took control of central Cairo and demonstrations against army rule erupted across the country.

In scenes reminiscent of the 18-day uprising that toppled Hosni Mubarak earlier this year, civilian-run popular committees commanded all entrances and exits to Tahrir Square, while government security forces were nowhere to be seen.

In a massive show of public anger at the slow pace of reform under military rulers, demonstrators chanted repeatedly for the ousting of the country's de facto ruler, Field Marshal Mohamed Hussein Tantawi. They called on Egyptians to "reclaim" their revolution. Activists declared the start of an open-ended sit-in, vowing not to leave until post-Mubarak transition was put back in the hands of ordinary people.

"This is not just another Friday protest – it's a message to the Supreme Council of the Armed Forces [Scaf] that their methods don't work and that we are immune to their tricks and lies," said Wael Eskandar, a 27 year old IT consultant who joined the protests in Cairo. "No matter how much they try spreading disinformation and claim the army is trying to implement the demands of the revolution, Egyptians know the real deal – and that is why you see so many here today."

In Egypt's second city, Alexandria, tens of thousands gathered and held up mock nooses alongside dummies of Mubarak and several of his former ministers, as well as dummies of other regime-era officials who have yet to be removed from their jobs. Large demonstrations took place in the industrial city of Suez, the scene of violent clashes earlier this week between protesters and riot police, while in Luxor thousands more gathered under the city's most famous Pharaonic temple to express their dissatisfaction with the interim authorities.

"It's the biggest show of force against the military thus far," said Shadi Hamid, director of research at the Brookings Doha Centre and an expert on Egyptian politics. "Until recently, the army had very high favourability ratings, and Egyptians had been reticent to criticise it too openly, but now we're seeing the emergence of competing legitimacies.

"The generals claim to represent the revolution and the will of the people but today the protesters in Tahrir and beyond are saying no: we are the ones that represent the revolution, we are the legitimate representatives of the people. It's a growing divide between the two sides, and it can only lead to more confrontation."

In Cairo's Tahrir Square, street vendors sold home-made gas masks as crowds began to muster under the sweltering midday heat. But the security forces that had attacked protesters there only last week, firing multiple teargas canisters and injuring more than 1,000 people, remained out of sight.

In a sign that protesters are seeking not just to oppose the new political establishment but to provide an alternative, questionnaires about the future of Egypt were handed out and then placed in manned ballot boxes, while "voters" had their thumbs marked with indelible ink.

Delegations from Egypt's nascent independent labour unions also joined the rally, despite a boycott from the official, state-controlled trade union congress. Camera crews from state television channels were forcibly ejected from the square because of their perceived obeisance.

"There are specific demands – such as the speeding up of trials, holding police to account, and so on – but none of them individually quite capture what this is about today," said Khalid Abdalla, an actor. "The fundamental issue is that there is no one in authority speaking to these people and making them feel secure in this transitional period. So, instead, people are speaking for themselves, and a broad consensus about the need for change is forming. That consensus is clearly pitted against the army."

Most experts believe there is little chance of the military drastically changing direction and pursuing vigorous reform. "SCAF is not a pro-democracy organisation: they don't care much about the revolution per se – what matters to them is security and stability, and there really is no ideological content in their actions," argued Hamid. "They can't all of a sudden embrace full democracy because that would go against their interests as an institution, so I don't even know if the military is capable of doing what the protesters want it to do."

Hamid said that Egypt's interim leader was now beginning to look vulnerable. "Tantawi is not quite on par with Mubarak in people's eyes, but he's getting there. If he ever had any chance to protect his legacy and go out as someone who helped facilitate Egypt's revolution, then I think he's losing that now, so there's a lot at stake for him."